Re: AMBER: MD at different pH !!

From: Bimo Ario Tejo <>
Date: Sat, 6 Mar 2004 13:18:15 +0100 (MET)

Hi Jiten,

You should neutralize your system, particularly if you use PBC. If the
system doesn't have a neutral charge, then when you replicate it using PBC, the
total charge would become infinity.


> Thanks for the discussion on MD at different pH. When we assign the
> charges
> on the residues at different pH the total charge of the protein would be
> changed. According the sander MD simulations, it would force plasma charge
> neutrailty. In such case should we need to neutalise the systems with
> counterions before the simulation - I mean using xleap.
> Your advice to me would be highly appreciated, Thanks in advance.
> Jiten

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Received on Sat Mar 06 2004 - 12:53:01 PST
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